[quote=Sloth]
But the extended cut says everything turns out dandy!Why would Bioware lie to me? 
[/quote]

Because BioWare crapped out the ending super quickly because their lead writer left before they could finish London and needed to throw something together quicker than a Chinese sweat shop. Or, alternatively, if you want to be less cynical, you can imagine that's what's going through Shepard's head, which is conflicting with the actual reality, kind of in the same way that that Saren husk was no longer Saren at the end of ME1.